Using PGP as part of a filter makes perfect sense. If you're looking for "bad guys" that do certain activities, as a starting filter, it doesn't hurt to say "OK, show me everyone in this region doing these activities. Now filter by language, etc. etc.".
Just like if I was looking for gang members, I might start off a filter with "look for tattoos". It doesn't mean I'm saying everyone with a tattoo is gang member, it's just a way to start filtering.
The NSA analysts are presumably actually trying to get something done (find people they think are bad). How stupid do you think they are? If you were an NSA analyst, would you tag "person of interest" on everyone using PGP? How would that help your goal of finding actual people of interest?
They say they caught 300 "terrorists" with this program and other success stories. Presumably, they didn't achieve any success by wasting lots of time flagging random PGP users.
If yesterday we were "conspiracy theorists" when we suspected things like XKeyscore, what are we today if we suspect things like "Person of Interest"-like programs?
"You are being watched. The government has a secret system: a machine that spies on you every hour of every day. I know, because I built it. I designed the machine to detect acts of terror, but it sees everything. Violent crimes involving ordinary people; people like you. Crimes the government considered 'irrelevant'. They wouldn't act, so I decided I would. But I needed a partner, someone with the skills to intervene. Hunted by the authorities, we work in secret. You'll never find us, but victim or perpetrator, if your number's up... we'll find you".
It's in the full presentation linked at the top of the article. Under the heading "Finding Targets", "someone who is using encryption" is one of the listed means of identifying someone for targeting (along with "someone whose language is out of place for the region they are in"…).
